Biosynthetic enzyme complexes selectively catalyze challenging chemical transformations, including alkane functionalization (e.g., halogenation of threonine, Thr, by non-heme iron SyrB2). However, the role of complex formation in enabling reactivity and guiding selectivity is poorly understood, owing to the challenges associated with obtaining detailed structural information of the dynamically associating protein complexes. I will discuss how long-time classical molecular dynamics of SyrB2 and the acyl carrier protein SyrB1 and large-scale QM/MM simulation provide insight into substrate–protein and protein–protein dynamics that give rise to experimentally observed substrate positioning and reactivity trends. I will describe dynamics that lead to a transient opening of the hypothesized substrate-delivery channel for phosphopantetheine (PPant)-bound substrates in SyrB2 through free energy simulations. I will describe how we overcome some of the limitations of approximate classical force fields by sampling metal–substrate distances observed in experimental spectroscopy of native SyrB2/SyrB1-PPant-S-Thr and non-native substrates. This approach allows us to identify essential protein–substrate interactions that are responsible for substrate positioning, and thus, reactivity. Specifically, we observe the hydroxyl sidechain and terminal amine of the native Thr substrate to form cooperative hydrogen bonds with a single N123 residue in SyrB2 in contrast to non-native substrates that can orient closer to the Fe center. These differences have the potential to explain the experimentally-observed divergence in native and non-native substrate reactivity. This computational/theoretical talk will be presented adjacent to a talk on the insight gained from experimental structural characterization of non-heme Fe enzymes.

Understanding the protein's role in substrate positioning and reactivity with simulation: Case of SyrB2/SyrB1

2019 Fall National Meeting

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